Archive by Author | Rob

We <3 New York Botanic Gardens (NYBG) and the first NitFix expedition finished

Back in October, we started an adventure that I am not sure has ever been tried before. We aimed to sample 15,000 species (!) of nitrogen fixing plants, with the goal of assembling one of the largest set of resources to better understand the underlying genomic innovations that led to nitrogen-fixing plants. The main resource we are using are small tissue samples (e.g. leaf and floral material) taken from already-collected samples stored in herbaria. Our first port of call was the New York Botanic Gardens, and the truly awesome staff there, especially Barbara Theirs and Charlie Zimmerman, but we owe thanks to the whole herbarium for making us feel so welcome.  We ❤ NYBG!

Here we are happily sampling:

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We collected about 1400 samples during our first visit, and we since have also begun to extract DNA from those samples. The great news is that we are having a lot of success with extractions, thanks to the hard work of Heather Rose Kates at the Florida Museum. We will talk more about the next steps in further blog posts, but we are excited about that success. We have also visited a lot more herbaria, including ones at Harvard University, the California Academy of Sciences, the Missouri Botanic Gardens, and the Ohio State University. We also just headed back to the New York Botanic Gardens and will be sampling there for many more weeks. We anticipate hitting our half way mark this week – 7500 samples!   That represents a huge amount of work!

The data we are getting from labels is really important for this work. Photo vouchers and labels link the genes to the specimen, both virtually and in a physical sense too. Label data will be used in a lot of the downstream analyses that come from this work and we are so thrilled that you helping this science happen. Nitrogen fixing is a key novel symbioses that really changed the world, we are hoping to learn how that novelty arose, and herbaria and their specimens may be an essential part of the key to telling that story. Your help is so important so a HUGE thanks for your work on the first NitFix expedition. There is already a second one up and a third one soon to follow.


Talking about Talk

We are excited to see all the effort on Notes From Nature in terms of transcription effort, but one thing we’ve mentioned less is just how active everyone has been on Talk.  But the numbers are insane, in the good way.  Today was a record breaking day (we are currently at 203 talk items as of 5pm), and to just get a sense of activity change, below is the talk items per day chart for the past few months (from June 23-November 1).

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To what do we attribute all the talking, especially the big change in the last few weeks?  We aren’t sure, but whatever it is, its great to see.  We love the talking, and we appreciate all your help and willingness to share thoughts, concerns and expertise on the talk channels.


Too many eyes and legs!

We have a new expedition up on SPIDERS just in time for Halloween.  Spiders often get a bad rap. They are seen as scary and creepy, especially around Halloween when people decorate their houses and shrubs with fake webs and giant black widows. But spend a few minutes watching them and you will realize spiders are some of the most fascinating and talented animals in your neighborhood. The most conspicuous spiders are the orb weavers that spin webs of concentric circles, like in Charlotte’s Web – though don’t expect to see any advertisements written in these webs. Many of these spiders eat their webs each day, recycling the materials, and rebuild them for the next night’s catch, which they skillfully wrap in silk to snack on later.

Araneus sp _ SD Zoopicture credit San Diego Zoo

Many spider species do not build webs at all. Jumping spiders and wolf spiders are active, visual predators with two, large, forward-facing eyes, to go with their lateral eyes. They capture their prey by pouncing on them. Jumping spiders in particular are very inquisitive and often will investigate objects you set in front of them. Many are brightly colored and have very elaborate courtship displays in which they wave their front legs and thump their abdomens (try a search for “peacock spiders”).

Phidippus sp_Susan Kennedypicture credit Susan Kennedy

Spiders also are unfairly accused of bites and crawling into people’s mouths at night. It is not clear where these urban myths came from, but there is no evidence that spiders infiltrate us while we slumber. As far as bites, it is extremely rare that someone actually finds the suspected spider on, or anywhere near them after a bite. Unless a spider feels trapped with no recourse, it very rarely bites. Even when left with the choice of fighting back or losing a leg, many will choose to lose a leg and run away on seven.

So why the bad rap? Probably because we walk into their sticky webs and find them lurking in the corners of our buildings. And also because they look so incredibly different from us with too many legs and too many eyes.

Finally, thanks for your help with our newest CalBug expedition, although maybe in this case we should call it SpiderCal or ArachniCal for this one instead?

Peter Oboyski, with slight embellishment by Rob Guralnick


Thanks for your help on the “New World Swallowtail Butterflies from the Field Museum of Natural History II” expedition

Butterfly wings are amazing things, made of two connected membranes, with internal nerves, veins and passages for air inside.  On the outside are pigmented scales that attach to this membrane.  Those pigmented scales give butterflies their vibrant colors that continue to amaze us.  When flying, wings are moved by the rapid muscular contraction and expansion of the thorax, providing lift.  

Scales of a butterfly wing.  Photo from:

The shape of butterfly wings have been sculpted by selective forces, both natural and sexual selection.  How wing shape varies due to biotic and abiotic factors has long fascinated biologists, including my post-doctoral student, Hannah Owens.  She has been working on one of the largest accumulations of butterfly wing morphometrics yet attempted, that includes 1000s of specimens.  One reason we can do this work is because of volunteer help transcribing labels that describe where these specimens were collected. With that information, we can also get information on the environment where those specimens were collected.

  We really appreciate the effort to accelerate research on butterfly wing shape, and we’ll be talking more about her work, especially some key questions she can tackle, in a later blog post.   We have another set of images soon available and more about this neat work she is doing. Thanks for your effort to be part of Hannah and her research project, and for being part of Notes of Nature.   We have some more images coming – what we think might be the last batch – and we hope you’d be willing to help again.


Thanks for talking

We’ve mentioned recently that we’ve been thrilled to see more effort on Notes from Nature in terms of transcriptions.  We also wanted to mention that there has been an equally strong uptick on the talk channels.  We want to encourage everyone to talk about the objects, connect with like minded folks, etc. We really appreciate the feedback.  As extra encouragement, we are now offering two new badges, the “Communicator” badge, for posting one item on “talk” of any sort,  and the “Socializer” badge, for 25 posts.   Rather than spoil the fun, we are going to keep the badges a surprise for now, but encourage you to get those badges!


Why all the swallowtail butterflies?

You may have noticed that there have been a few different expeditions in the past few months focused on swallowtail butterflies. These specimens will be used for a larger project where we are planning to quantitatively look at the variation in wing morphology across and within swallowtail butterfly species. We have amassed approximately 1300 photos of swallowtail specimens from various museum and personal collections with the intention of having at least 10 males and 10 females from every Papilio species. Using morphometric analyses of landmarks on the dorsal and ventral wings, we will test the wing shape variation across species to see if there are correlations with sex, tropicality, geographic range size, and the number of congeners in the species’ range.

What do we mean by “landmarking”? This is an approach called “geometric morphometrics” where we select the same locations on a butterfly image in each image, and then we use some really neat tools that can find the best “fit” to a common “consensus”. For this project, we are using where veins in the butterfly wings meet the edge as our landmarks. Figure 1 shows an example of the ventral wing landmarks using this fitting method. The big black dots are the “consensus” landmarks and the variation around them in shown in the smaller grey ones. You can clearly see that some parts of the wing are much more variable than others. We know the orientation of the image below is a bit odd, but the variable landmark that is at the low point on the y-axis is near where the wing attaches to the body.

Now that all of the Notes from Nature swallowtail expeditions are complete, we will be working all summer to landmark these specimens and add more to our sample size for future analyses. If you are interested in the further ways we analyze morphological variation, give a holler and we can go into further detail. We will send along another update on this work later in summer, and thank you for helping us move forward with this research!

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Figure 1. Plot for the x/y coordinates of the ventral wing landmarks for 27 Papilio specimens so far.

blog post by Laura Brenskelle


Almost there… a finishing challenge

We are running a new expedition finishing challenge, for those with completion anxiety (like we do).  Here are the expeditions closest to finished, in near order of effort needed:

1. Butterfly_New World Swallowtail Butterflies II

Classifications: 433 / 609, 71% complete but only 175 or so transcriptions left.

2. Herbarium_Unlocking Northeastern Forests: Nature’s Laboratories for Global Chang

Classifications: 6,886 / 7,089, 97% complete (200+ left)

3. Herbarium_Amaranthaceae: Cosmopolitan Allrounder

Classifications: 981 / 1,332, 74% complete (~350 transcriptions left)

3. Herbarium_Natural North Carolina’s – Adoxaceae – Elderberry and Viburnum!

Classifications:  8,480 / 9,288, 91% complete (still 700 left)

We really appreciate the help, and we’ll report when these get finished, so you can see who wins the challenge!

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